Compositions and methods for probiotic recolonization therapies

ABSTRACT

The present invention relates to pharmaceutical compositions suitable for the treatment of chronic diseases associated with the presence of abnormal or an abnormal distribution of microflora in the gastrointestinal tract of a mammalian host, which compositions comprise viable non-pathogenic or attenuated pathogenic Clostridia. The compositions further comprise one or more additional viable non-pathogenic or attenuated pathogenic microorganisms selected from the group consisting of  Bacteroides , Eubacteria, Fusobacteria, Propionibacteria, Lactobacilli, anaerobic cocci,  Ruminococcus, E. coli, Gemmiger, Desulfomonas, Peptostreptococcus , and fungi. The present invention also provides pharmaceutical compositions suitable for the treatment of the same chronic diseases comprising viable non-pathogenic or attenuated pathogenic  Escherichia coli , at least one strain of viable non-pathogenic or attenuated pathogenic  Bacteroides  and at least one strain of viable non-pathogenic or attenuated pathogenic microorganism.

CROSS-REFERENCE TO RELATED APPLICATIONS

This United States utility patent application is a continuation of U.S.Ser. No. 13/910,579, filed Jun. 5, 2013 (now pending), which is adivisional of U.S. Ser. No. 10/332,986, filed Aug. 4, 2003, now U.S.Pat. No. 8,460,648, issued Jun. 11, 2013 which is a §371 national phaseof PCT international patent application no. PCT/AU01/00907, having aninternational filing date of Jul. 25, 2001, which claims benefit ofpriority to Australian Patent Application Serial No. PQ 8997, filed Jul.25, 2000. The aforementioned applications are expressly incorporatedherein by reference in their entirety and for all purposes.

TECHNICAL FIELD

The present invention relates to pharmaceutical compositions suitablefor the treatment of diseases in mammals, in particular to the treatmentof chronic disorders associated with the presence of abnormal or anabnormal distribution of microflora in the gastrointestinal tract. Theinvention also relates to methods of treating such diseases.

BACKGROUND ART

There are large numbers of patients suffering from gastro-intestinalsymptoms referable to the lower small bowel and large bowel which todate have eluded explanation, These disorders include irritable bowelsyndrome (IBS) or spastic colon, idiopathic ulcerative colitis, mucouscolitis, collagenous colitis, Crohn's disease, inflammatory boweldisease in general, microscopic colitis, antibiotic-associated colitis,idiopathic or simple constipation, diverticular disease, and AIDSenteropathy. Pathophysiology of these disorders eludes logicalexplanation in spite of decades of research and millions of dollars ofresearch funds. A common underlying factor shared by all these disordersobserved by the present inventor is their onset or aggravation followingsome extraneous invading infection e.g., traveler's diarrhea. In all thedisorders, a specific causal infection generally cannot be demonstrateddue to our inability to detect infecting agents whose culturalcharacteristics are unknown to medical science.

Circumstantial evidence which suggests that these disorders are“infection-related” includes: (a) onset following a gastro-intestinalinfection which failed to completely resolve; (b) transient improvementwith use of certain antibiotics, but recurrence upon cessation ofantibiotics; (c) transient improvement following orthostatic lavageprior to colonoscopy and; (d) transient symptom improvement with use of“colonic” irrigation.

It is impractical to use long-term antibiotic therapy (with itsassociated complications) in such patients since cure is not obtainedwith its use. Furthermore, chronic gut infections with recognized,specific pathogens such as Clostridium difficile, Yersiniaenterocolitica or Campylobacter jejuni/coli are generally not eradicatedwith antibiotics. Some previous attempts have been made to alter theenteric microflora in order to eradicate such chronic infections. Thesemeasures nevertheless indicate that alteration of bacterial flora mayeffect dramatic clinical improvement in conditions characterized bychronic, resistant enterocolitic infection. However there remain manychronic disorders of uncertain aetiology or causation, which areresistant to cure by current therapeutic techniques.

The use of probiotics in the human population has been largely confinedto. the inclusion in various foods of live organism of Lactobacilli andBifidobacteria and less frequently Streptococcus faecalis or severalstrains of Escherichia coli. These organisms are thought to promotehealth via immune stimulation and reconstitution of what is presumed tobe normal flora. Such usage stems back to the beliefs generated byMechnikov in the early 1900s. The use of probiotics to treat establishedinfections in the gastrointestinal tract has been lesser but a growingpart of the use of probiotics. Fungal agents such as Saccharomycesboulardii have been used to treat, albeit inefficiently, Clostridiumdifficile infection and Lactobacillus GG has also been used for thispurpose (Floch M. Probiotics and Dietary Fibre. J Clin Gastroenterol1998; 27(2):99-100). Various patents have claimed the use of probioticsfor narrow disease conditions including treatment of Clostridiumdifficile with a combination of Vancomycin and butyric acid bacteria(U.S. Pat. No. 5,266,315), diarrhea prevention using Lactobacillus (U.S.Pat. No. 5,837,238) or Bifidobacterium (U.S. Pat. No. 5,902,743),Lactobacillus acidophilus to inhibit cryptosporidium (U.S. Pat. No.5,858,356) and mixtures of Lactobacilli and Bifidobacteria in infants toprevent diarrhea. Enterococcus faecium has been claimed to be useful inalleviating symptoms of Irritable Bowel Syndrome in humans (U.S. Pat.No. 5,902,578) (U.S. Pat. No. 5,728,380) but this has not recognizedClostridium as the underlying agent in this condition. Clostridiumbutyricum as a single agent has been claimed to be a biologicalintestinal antiseptic for treatment of bacterial food poisonings (U.S.Pat. No. 4,892,731), but its use in chronic disease treatment was notcontemplated.

Previous attempts to alter the enteric microflora of a patient haveprescribed the removal of at least a part of the host's existing entericmicroflora, for instance by lavage, prior to substitution withpredetermined desired microflora. This procedure, which was thepreferred embodiment of WO90/01335 has the distinct disadvantages ofcomplicating the treatment and of causing further discomfort to thepatient. This patent also advocated the use of dried, reconstitutedfaeces or a synthetic mixture comprising Bacteroides sp. and Escherichiacoli. It has now been surprisingly found that lavage or other methods ofremoval of at least a part of the host's existing enteric microflora canbe omitted provided a non-pathogenic Clostridium sp. is included withinthe probiotic replacement mixture. Such a replacement mixture has thedual ability of displacing pathogenic bacteria, frequently Clostridialin nature and also establishing a normal environment in which commensalbacteria can establish. Such a treatment permits long-term recovery bothfrom gastrointestinal disorders and from systemic afflictions nothitherto considered to be caused by harmful enteric flora. These arealso called ‘para-infective’ phenomena and can include rheumatological,neurological, regressive, hepatic, and dermatological conditions amongothers.

Autism is a regressive disorder of childhood, affecting boys four timesmore often than girls. It has been observed that the onset of autism isoften preceded by broad spectrum antibiotic use e.g. for recurrent earinfections. Antibiotic therapy is non-discriminatory in its action andapart from treating the ear infection the microflora of the healthygastrointestinal tract can be severely disrupted by such treatment. Thiscreates an environment where vulnerability to opportunisticmicroorganism colonization is heightened.

Clostridium tetani is a widely distributed, spore forming anaerobe.Toxigenic strains of Clostridium tetani produce the extremely potenttetanus neurotoxin which is known to enter the central nervous systemfrom the intestinal tract via the vagus nerve (Hensel B et al. NaunynSchmeidebergs Arch Pharmocol 1973; 276:395). Bolte (Med Hypotheses 1998;51:133) has hypothesized that opportunistic infection by Clostridiumtetani may be responsible for the behavioral and medical symptomspresent in a sub-group of individuals diagnosed with autism. Others havealso raised the possibility of clostridia in general as a cause ofdisease (Borriello S P. Clin Infect Dis 1995; Suppl 2:5242).

Sandier et al. (Fourth Int. Symp. Brain-Gut Interactions. 1998; 10: 363)report a trial in which children with delayed onset autism were treatedwith vancomycin over an 8 week period. All children in the trial had hadantecedent broad-spectrum antibiotic exposure, followed by chronicpersistent diarrhea and then onset of autistic features. Althoughsignificant post-treatment improvement was noted, all childreneventually regressed towards baseline.

It is on the background of these known facts and later the results oftrials of treatment, that the present invention was formulated. Inbrief, it was noted that autistic children (as well as relatedsyndromes) who were referred for treatment of refractory ‘irritablebowel syndrome’ (IBS) viz diarrhea, flatulence, constipation,distension, abdominal pains etc—responded to treatment of their IBS whentreated with a novel mix of probiotics. However, not only did their IBSimprove dramatically but also their autistic features progressivelyregressed. Even after the initial 2-6 weeks of treatment eye contact wasre-established, repetitive movements were much reduced, and word power(observed vocabulary) expanded—initially 20 words and ultimately >600words at 12 months (estimated), creating ability of the autisticchildren to form long sentences. Continuing improvement was observed tooccur over 12 months of treatment. These observations (to a lesser butdefinite degree at this stage of observations) also applied to thosewith Rett syndrome and children with Attention Deficit/HyperactivityDisorder (ADHD), Attention Deficit Disorder (ADD), and autism variantAsperger's syndrome. The observations strongly suggest that thetreatment of presumed enteric infection/s (e.g. Clostridial) in theseconditions not only improves the IBS present but also the attendantneurological ‘para-infective’ phenomena called collectively autism,Asperger's, Rett syndrome, ADD or ADHD.

The inclusion within this specification of reference to publisheddocuments is not to be taken to be an admission that any one or more ofthose documents, nor the disclosure of any one or more of thosedocuments, is part of the common general knowledge.

OBJECTS OF THE INVENTION

It is thus an object of the present invention to provide novelpharmaceutical compositions suitable for the treatment of variousdisease states related to the presence of ‘abnormal’ microflora in thegastrointestinal tract. It is a further object of the invention topropose the use of these pharmaceutical compositions in various diseasestates which have not previously been considered to owe their causationto the presence of abnormal flora in the gastrointestinal tract.

DISCLOSURE OF THE INVENTION

The present invention recognizes chronic infection/infestation as theunderlying pathological process in a wide range of chronic disorderssuch as irritable bowel syndrome, particularly when characterized bychronic abdominal pain, bloating, or excessive flatulence, together withchronic diarrhea or alternating constipation/diarrhea, and also inspastic colon, mucous colitis, collagenous colitis, ulcerative colitis,Crohn's colitis, microscopic colitis, idiopathic inflammatory boweldisease, antibiotic-associated colitis, idiopathic or simpleconstipation, diverticular disease and AIDS enteropathy.

The invention has also been found to relate to other gastrointestinaldisorders of unexplained aetiology such as polyposis coli and colonicpolyps, which may well be influenced by the local bowel microflora.

In addition the present invention also provides a method of treatment ofchronic gastrointestinal infections with specific microorganisms such asClostridium difficile, Yersinia spp, Campylobacter spp, Aeromonas spp,Escherichia coli, Cryptosporidium spp, Amoebae, Blastocystitis hominis,Giardia and even chronic viral infections, and of small bowel bacterialovergrowth.

The present invention furthermore, recognizes the close associationbetween the intestine and liver disease, and the intestine and migrainesand chronic fatigue syndrome, and possibly other neurological syndromessuch as, multiple sclerosis, amyotrophic lateral sclerosis, myastheniagravis, Parkinson's disease, Alzheimer's disease, Chronic InflammatoryDemyelinating Polyneuropathy (CIDP), Guillain Barre Syndrome, and otherdegenerative disorders. Hence, it is proposed that a considerableproportion of currently unexplained diseases of the liver and nervoussystem of unknown aetiology may be explicable by the chronic growth ofpathogens within the small/large intestine and the subsequent passage ofantigenic material, pathogenic toxins or biological response modifiers(BRMs) into the portal system (liver damage) or systemic circulationwith antibody formation (neurological conditions). Specifically, suchhepato/biliary system disorders as primary biliary cirrhosis, primarysclerosing cholangitis, fatty liver of unknown aetiology, or cryptogeniccirrhosis, may be secondary to chronic pathogen carrier state in theintestine.

The links between the intestine and joint disease are also recognised.Joint diseases such as rheumatoid arthritis, the non-rheumatoidarthritidies including, ankylosing spondylitis, and Reiter's syndrome,may also be causally related to a chronic intestinal carrier state, asmay other syndromes with an immune mediated component such asglomerulonephritis, haemolytic uraemic syndrome, juvenile diabetesmellitus, Behcet's syndrome, coeliac disease and dermatitisherpetiformis. Similarly, syndromes with an immune complex mediatedcomponent, such as scleroderma, systemic lupus erythematosus, mixedcryoglobulinaemia, polyarteritis, familial Mediterranean fever,amyloidosis, and the various presentations of such syndromes, togetherwith such “idiopathic” states as chronic urticaria, may bemanifestations of variations of immune regulated responses to relatedbowel-origin pathogens chronically shedding their antigen(s), toxins orbiological response modifiers into the circulation. Other chronicconditions such as acne, and chronic idiopathic pseudo-obstructivesyndrome, may well be influenced by similar mechanisms.

For many of these syndromes present therapy offers only palliation ofsymptoms and/or the induction of remission of the disease process butnot cure. The present inventor therefore recognised the need to find acurative therapy for these wide ranging disease processes associatedwith considerable morbidity.

By judicious selection of the microorganisms of the invention it hasbeen surprisingly found by the present inventor that lastingdecolonization of the gut microflora does not require pretreatment toremove a portion of the host's existing enteric microflora. Thus, byincorporation of Clostridia spp. in the therapy, it has beensurprisingly found that the prior art requirement for removal of atleast a portion of the existing enteric microflora before administrationof the substitute microflora is rendered unnecessary. Without theaddition specifically of Clostridia species, the use of probioticmixtures, e.g. such as those of Bacteroides and Escherichia coli failedto have the necessary impact on the above-mentioned clinical disordersfor the treatment to be clinically useful. It required a prior purgingof the gut of its presumably infected and abnormal bowel flora, recolonization with bacteroides and Escherichia coli—the main componentsof lower intestinal tract, and ongoing feeding of patients with suchbacteria until colonization was established. The use of Clostridiaappears to be the mainstay of this new therapy and the Clostridia appearto have power of themselves to remove offending bacterial species whichmay be responsible for the underlying condition (presumably pathogenicclostridia—yet to be identified scientifically). Hence, the combinationof non-pathogenic clostridia together with the crucial major colonicbacterial components of bacteroides and Escherichia coli can now be usedas oral therapy to crowd out/destroy/replace and recolonize thedysbiotic flora of patients with various gastrointestinal conditionswhich are caused by abnormal bowel flora. In fact, such a therapybecoming available has permitted or allowed greater understanding of thepathogenesis of many other conditions which hitherto were thought to becaused by degenerative, inflammatory, or auto immune mechanisms.

Thus according to a first embodiment of the invention there is provideda pharmaceutical composition useful for the treatment and/or prophylaxisof chronic disorders associated with the presence in thegastrointestinal tract of a mammalian host of abnormal or an abnormaldistribution of microflora, which composition comprises viablenon-pathogenic or attenuated pathogenic Clostridia.

Typically the composition includes Clostridia selected from the groupconsisting of Clostridium absonum, Clostridium argentinense, Clostridiumbaratii, Clostridium bifermentans, Clostridium botulinum, Clostridiumbutyricum, Clostridium cadaveris, Clostridium carnis, Clostridiumcelatum, Clostridium chauvoei, Clostridium clostridioforme, Clostridiumcochlearium, Clostridium difficile, Clostridium fallax, Clostridiumfelsineum, Clostridium ghonii, Clostridium glycolicum, Clostridiumhaemolyticum, Clostridium hastiforme, Clostridium histolyticum,Clostridium indolis, Clostridium innocuum, Clostridium irregulare,Clostridium limosum, Clostridium malenominatum, Clostridium novyi,Clostridium oroticum, Clostridium paraputrificum, Clostridiumperfringens, Clostridium piliforme, Clostridium putrefaciens,Clostridium putrificum, Clostridium ramosum, Clostridium sardiniense,Clostridium sartagoforme, Clostridium scindens, Clostridium septicum,Clostridium sordellii, Clostridium sphenoides, Clostridium spiroforme,Clostridium sporogenes, Clostridium subterminale, Clostridium symbiosum,Clostridium tertium, Clostridium tetani, Clostridium welchii,Clostridium villosum.

In a preferred form the composition further comprises one or moreadditional viable non-pathogenic or attenuated pathogenic microorganismsselected from the group consisting of Bacteroides, Eubacteria,Fusobacteria, Propionibacteria, Lactobacilli, anaerobic cocci,Ruminococcus, Escherichia coli, Gemmiger, Desulfomonas,Peptostreptococcus species and, more specifically, bacteria selectedfrom Table 1. Preferably fungi are also present such as Monilia.

In a preferred form the composition comprises Clostridia, Bacteroides,Peptostreptococcus, Escherichia coli, Bifidobacterium, andLactobacillus.

In a more preferred form the composition comprises Clostridium innocuum,Clostridium bifermentans, Clostridium butyricum, Bacteroides fragilis,Bacteroides thetaiotaomicron, Bacteroides uniformis, one or more strainsof Escherichia coli, and one or more strains of Lactobacillus.

Alternatively, in a preferred form the composition comprises Clostridiumbifermentans, Clostridium innocuum, and Clostridium butyricum incombination one or more strains of Escherichia coli, one or more strainsof bacteroides and Peptostreptococcus productus,

According to a second embodiment of the invention there is provided apharmaceutical composition useful for the treatment and/or prophylaxisof chronic disorders associated with the presence in thegastrointestinal tract of a mammalian host of abnormal or an abnormaldistribution of microflora, which composition comprises viablenon-pathogenic or attenuated pathogenic Escherichia coli, at least onestrain of viable non-pathogenic or attenuated pathogenic Bacteroides,and at least one other viable non-pathogenic or attenuated pathogenicmicroorganism.

In a preferred form the other viable non-pathogenic or attenuatedpathogenic microorganism is selected from the group consisting ofClostridia, Peptostreptococcus, Bifidobacterium, and Lactobacillus.

Typically the composition of the first or second embodiments of theinvention is derived from disease screened fresh homologous faeces,equivalent freeze-dried and reconstituted faeces or a “synthetic” faecalcomposition. The fresh homologous faeces does not include an antibioticresistant population.

Typically, the composition of the first or second embodiments of theinvention is a synthetic faecal composition.

In a preferred form the synthetic faecal composition comprises apreparation of viable flora which preferably in proportional content,resembles normal healthy human faecal flora which does not includeantibiotic resistant populations. Suitable microorganisms may beselected from the following: Bacteroides, Eubacteria, Fusobacteria,Propionibacteria, Lactobacilli, anaerobic cocci, Ruminococcus,Escherichia coli, Gemmiger, Clostridium, Desulfomonas,Peptostreptococcus, Bifidobacterium, species and, more specifically,bacteria selected from Table 1. Preferably fungi are also present suchas Monilia.

In a preferred form the composition of the first or second embodimentsof the invention comprises a liquid culture.

Preferably, the composition of the first or the second embodiments ofthe present invention is lyophilized, pulverized and powdered. It maythen be infused, dissolved such as in saline, as an enema.

Alternatively the powder may be encapsulated as enteric-coated capsulesfor oral administration. These capsules may take the form ofenteric-coated microcapsules. As a powder it can preferably be providedin a palatable form for reconstitution for drinking or forreconstitution as a food additive. The composition can be provided as apowder for sale in combination with a food or drink. Typically, the foodor drink is a dairy-based product or a soy-based product. The inventiontherefore also includes a food or food supplement containing acomposition according to the first or second embodiment. In a preferredform the food or food supplement contains enteric-coated microcapsulesof the composition of the invention. In a preferred form the food isyogurt.

The powder may be reconstituted also to be infused via naso-duodenalinfusion. The composition can be combined with other adjuvants such asantacids to dampen bacterial inactivation in the stomach., e.g. Mylanta,Mucaine, Gastrogel. Acid secretion in the stomach could also bepharmacologically suppressed using H2-antagonists or proton pumpinhibitors. Typically, the H2-antagonist is ranitidine. Typically theproton pump inhibitor is omeprazole.

The composition of the first or second embodiments of the invention istherefore preferably in the form of:

an enema composition which can be reconstituted with an appropriatediluent, or

enteric-coated capsules, or

enteric-coated microcapsules, or

powder for reconstitution with an appropriate diluent for naso-entericinfusion or colonoscopic infusion, or

powder for reconstitution with appropriate diluent, flavoring andgastric acid suppression agent for oral ingestion, or

powder for reconstitution with food or drink, or

food or food supplement comprising enteric-coated microcapsules of thecomposition, powder, jelly, or liquid.

According to a third embodiment of the invention there is provided amethod for the treatment and/or prophylaxis of a chronic disorderassociated with the presence in the gastrointestinal tract of amammalian host of abnormal or an abnormal distribution of microflora,which method comprises administering an effective amount of acomposition according to the first or second embodiment of theinvention.

In its preferred form the treatment should effect a cure of the symptomsof such disorders. The change of flora is preferably as “near-complete”as possible and the flora is replaced by viable organisms which willcrowd out any remaining, original flora.

The method of the present invention is applicable to animals in general,in particular humans and economically significant domestic animals.

In the case of humans, the present invention encompasses methods oftreatment of chronic disorders associated with the presence of abnormalenteric microflora. Such disorders include but are not limited to thoseconditions in the following categories:

gastro-intestinal disorders including irritable bowel syndrome orspastic colon, functional bowel disease (FBD), including constipationpredominant FBD, pain predominant FBD, upper abdominal FBD, non-ulcerdyspepsia (NUD), gastro-oesophageal reflux, inflammatory bowel diseaseincluding Crohn's disease, ulcerative colitis, indeterminate colitis,collagenous colitis, microscopic colitis, chronic Clostridium difficileinfection, pseudomembranous colitis, mucous colitis, antibioticassociated colitis, idiopathic or simple constipation, diverticulardisease, AIDS enteropathy, small bowel bacterial overgrowth, coeliacdisease, polyposis coli, colonic polyps, chronic idiopathic pseudoobstructive syndrome;

chronic gut infections with specific pathogens including bacteria,viruses, fungi and protozoa;

viral gastrointestinal disorders, including viral gastroenteritis,Norwalk viral gastroenteritis, rotavirus gastroenteritis, AIDS relatedgastroenteritis;

liver disorders such as primary biliary cirrhosis, primary sclerosingcholangitis, fatty liver or cryptogenic cirrhosis;

rheumatic disorders such as rheumatoid arthritis, non-rheumatoidarthritidies, non rheumatoid factor positive arthritis, ankylosingspondylitis, Lyme disease, and Reiter's syndrome;

immune mediated disorders such as glomerulonephritis, haemolytic uraemicsyndrome, juvenile diabetes mellitus, mixed cryoglobulinaemia,polyarteritis, familial Mediterranean fever, amyloidosis, scleroderma,systemic lupus erythematosus, and Behcets syndrome;

autoimmune disorders including systemic lupus, idiopathicthrombocytopenic purpura, Sjogren's syndrome, haemolytic uremic syndromeor scleroderma;

neurological syndromes such as chronic fatigue syndrome, migraine,multiple sclerosis, amyotrophic lateral sclerosis, myasthenia gravis,Gillain-Barre syndrome, Parkinson's disease, Alzheimer's disease,Chronic Inflammatory Demyelinating Polyneuropathy, and otherdegenerative disorders;

psychiatric disorders including chronic depression, schizophrenia,psychotic disorders, manic depressive illness;

regressive disorders including Asperger's syndrome, Rett syndrome,attention deficit hyperactivity disorder (ADHD), and attention deficitdisorder (ADD);

the regressive disorder, autism;

sudden infant death syndrome (SIDS), anorexia nervosa;

dermatological conditions such as, chronic urticaria, acne, dermatitisherpetiformis and vasculitic disorders.

The above disorders are all characterized by their response to treatmentwith the method of the present invention.

Typically the change in enteric flora comprises introduction of an arrayof predetermined flora into the gastro-intestinal system, and thus in apreferred form the method of treatment comprises substantiallycompletely displacing pathogenic enteric flora in patients requiringsuch treatment.

Furthermore, in some of these disorders a short course of antibioticsprior to probiotic treatment may be preferred to rid tissue-invasivepathogens originating in the bowel lumen. For example, in Crohn'sdisease, anti-tuberculosis therapy may be required for six to twelveweeks before the bowel is cleared out and the flora content exchangedfor a predetermined flora.

Typically the antibiotic is an anti-Clostridial antibiotic such asvancomycin, rifampicin, and nitroimidazole or chloramphenicol. Typicallythe nitroimidazole is metronidazole.

In a preferred form of the invention, the method of treatment orprophylaxis further includes administration of at least one acidsuppressant prior to administering, or in co-administration with, thecomposition of the invention.

In a preferred form of the invention the method of treatment orprophylaxis further includes nasogastric and/or nasoduodenal washoutprior to administering said composition. The introduction of thecomposition into the gastro-intestinal system can be effected by enemaor per-colonoscope, via intubation of the small bowel using for examplea large bore catheter equipped with distal balloon to effect rapidpassage down the jejunum, or via the oral route with enteric-coatedcapsules, including enteric-coated microcapsules, or via the oral routewith a supplemented food or drink.

In a preferred form the supplemented food or drink is a dairy-based orsoy-based product. Typically the supplemented food product is yogurt.

According to the method of the invention each dose of the composition isin the range of about 10³ cells to about 10¹³ cells. Preferably eachdose is in the range of about 10⁵ cells to about 10¹¹ cells. Morepreferably each dose is in the range of about 10⁹ cells to about 10¹¹cells. In a preferred form of the invention an initial treatment regimenconsisting of about 10¹⁰ cells per dose is administered about 3 to 6times per day for a period sufficient to stabilize the gut flora.According to the method of the invention the treatment regimen may thencomprise a maintenance dose of about 10¹⁰ cells per day.

Furthermore the present invention also relates to the treatment ofanimals, in particular to the treatment of gastrointestinal disorders ineconomically important domestic animals, such as cattle, sheep, horses,pigs, goats etc. The method of the present invention has been found tobe especially useful in the treatment of the various forms ofnecrotizing enterocolitis which can be a major problem in animal stocks.

Obviously in the treatment of animals the appropriate composition ofmicroflora will vary according to the species being treated and theconstituent normal flora known to inhabit the gut.

Thus the composition according to the invention would comprise, apreparation of viable flora which preferably in proportional content,resembles the normal healthy faecal flora of the species involved. Thecompositions may be prepared in any of the forms already described andadministered accordingly.

Best Method of Performing the Invention

In the practice of the invention a synthetic faecal composition ofpredetermined flora in the form of a liquid or dry powdered culture ofClostridia, Bacteroides, Peptostreptococcus, Escherichia coli,Bifidobacterium, and Lactobacillus, which composition does not includeantibiotic resistant populations, is prepared as a liquid culture.Typically the method of the invention is applicable to a patientsuffering from a chronic disorder associated with the presence ofabnormal microflora in the gastrointestinal tract such as irritablebowel syndrome.

In the practice of the invention a composition of predetermined flora inthe form of a liquid culture of Clostridia, Bacteroides,Peptostreptococcus, Escherichia coli, Bifidobacterium, and Lactobacillusis ingested by the patient in an amount sufficient to replace andrecolonize the dysbiotic flora of the gastrointestinal tract, andreverse the disease process. Alternatively fresh homologous faecesobtained from a disease screened donor are liquefied and mixed withunprocessed bran. The mixture is then homogenized anaerobically underCO2 cover and infused into the patient per colonoscope.

Cure or remission of symptoms is then monitored subjectively and byassessment of stool frequency or other appropriate criteria.

Using liquid cultures of Clostridia, Bacteroides, Peptostreptococcus,Escherichia coli, Bifidobacterium, and Lactobacillus the inventor hasachieved total reversal of colitis, irritable bowel syndrome andconstipation.

As indicated in the method of treatment aspect of the invention, apreparatory course of appropriate antibiotics may be used. For example,Septrin for chronic yersiniasis, Metronidazole for ulcerative colitis,anti-TB therapy in Crohn's disease, or Vancomycin in chronic Clostridiumdifficile infestations.

TABLE 1 % of flora ″ Organism(s) 11.8(0.90)  Bacteroides fragilis ss.Vulgatus 9.9(0.83) Eubacterium aerofaciens 8.9(0.78) Bacteroidesfragilis ss. Thetaiotaomicron 6.6(0.68) Peptostreptococcus productus II6.0(0.64) Bacteroides fragilis ss. Distasonis 4.4(0.55) Fusobacteriumprausnitzii 3.5(0.49) Coprococcus eutactus 3.0(0.45) Eubacteriumaerofaciens 2.8(0.44) Peptostreptococcus productus 2.7(0.43)Ruminococcus bromii 2.6(0.43) Bifidobacterium adolescentis 2.2(0.39)Gemmiger formicilis, Bifidobacterium longum 2.1(0.38) Eubacteriumsiraeum 1.8(0.35) Ruminococcus torques 1.7(0.34) Eubacterium rectale1.6(0.33) Eubacterium rectale IV, Eubacterium eligens 1.5(0.32)Bacteroides eggerthii 1.4(0.31) Clostridium leptum 1.3(0.29) Bacteroidesfragilis ss. A 1.2(0.29) Eubacterium biforme 0.91(0.25)  Bifidobacteriuminfantis 0.84(0.24)  Eubacterium rectale 0.57(0.20)  Coprococcus comes,Bacteroides capillosus 0.50(0.18)  Ruminococcus albus, Eubacteriumformicigenerans, Eubacterium hallii, Eubacterium ventriosum I,Fusobacterium russii 0.43(0.17)  Ruminococcus obeum, Eubacterium rectale11, Clostridium ramosum I, Lactobacillus leichmannii 0.36(0.16) Ruminococcus, Butyrivibrio crossotus 0.30(0.14)  Acidaminococcusfermentans, Eubacterium ventriosum, Bacteroides fragilis ss. Fragilis;0.23(0.12)  Coprococcus catus, Eubacterium hadrum, Eubacteriumcylindroides, Eubacterium ruminantium, Eubacterium CH-1, Staphylococcusepidermidis 0.17(0.10)  Peptostreptococcus BL, Eubacterium limosum,Bacteroides praeacutus, Bacteroides L, Fusobacterium mortiferum I,Fusobacterium naviforme, Clostridium innocuum, Clostridium ramosum,Propionibacterium acnes, Ruminococcus flavefaciens 0.10(0.08) Ruminococcus AT, Peptococcus AU-1; Bacteroides fragilis ss. ovatus,Bacteroides -ss. d, Bacteroides -ss. f; Bacteroides L-1, BacteroidesL-5; Fusobacterium nucleatum, Fusobacterium mortiferum, Escherichiacoli, Streptococcus morbiliorum 0.05(0.05)  Peptococcus magnus,Peptococcus G, -AU-2; Streptococcus intermedius, Ruminococcus lactaris,Ruminococcus CO Gemmiger X, Coprococcus BH, -CC; Eubacterium tenue,Eubacterium ramulus, Bacteroides clostridiiformis ss. clostridiiformis,Bacteroides coagulans, Bacteroides oralis, Bacteroides rumlnicola ss.brevis, -ss. rumlnicola, Bacteroides splanchnicus, Desuifomonas pigra,Fusobacterium H, Lactobacillus G, Succinivibrio A ^(b) The percentage ofthe faecal population (the standard deviation of the estimate is givenin parentheses). The invention will now be further described withreference to the following non-limiting examples.

EXAMPLES Formulations

The probiotic therapeutic agents may be prepared in liquid cultureanaerobically or aerobically (depending on bacterium cultured) in pureform. Alternatively the probiotics may be cultured on solid media andscraped into a liquid carrier. The resulting product may be spray-driedinto a powder form and encapsulated or combined with excipients to bedelivered in sachets.

Combinations of Clostridia, Escherichia coli, Bacteroides, andPeptostreptococcus with or without Lactobacilli, Bifidobacteria andEubacteria may be used in varying disorders.

Example No 1 43 Year Old Female

Patient with long standing constipation not responsive to high-dosefiber usage together with prokinetics and standard anti-constipationtreatments, was treated with increasing doses of orally administeredbacterial mix (mixture composition included Clostridium innocuum,bifermentans, butyricum, together with Bacteroides fragilis,thetaiotaomicron and uniformis. Three strains of Escherichia coli werealso included, as was Lactobacillus). This was ingested twice daily inthe first two weeks and then daily thereafter. The patient was not givenany pre-treatment purgative nor any antibiotics. However, she did takeRanitidine (an acid suppressant) three hours prior to ingestion of thebacterial mix. Two weeks after commencing the treatment the patient'sconstipation—which would prevent her from defecating for up to fourdays—reversed to increased frequency with reduction of bloating.Initially, gas production increased and there was turbulence andgurgling in the abdomen but after four weeks of treatment the patientwas defecating on a daily basis with no sensation of incomplete emptyingand an almost total absence of bloating. Following the treatment sheremained virtually normal, defecating on a daily basis with 3 monthfollow up.

Example No 2 4¹Λ Year Old Male

Patient with 3 year history of diagnosis of autism associated withIrritable Bowel Syndrome characterized by constipation alternating withdiarrhea and flatulence, with foul motions, was treated with oraladministration of bacterial mix consisting of Clostridium bifermentans,Clostridium innocuum, and Clostridium butyricum in combination withthree strains of Escherichia coli, three strains of bacteroides andPeptostreptococcus productus. These were ingested following acidsuppression with Ranitidine and were at first taken 3 times daily,reducing to twice daily and then once daily maintenance for eight weeks.The patient's autistic symptoms were reversed quite dramatically withword power increasing from 20 to 200 words (counted by teacher atspecial ‘autistic’ school), he began to sleep through the night, and hisIBS-type symptoms reverted to near-normality with less constipation,less diarrhea and less foul flatulence. He developed eye contact, wasable to speak sentences up to six words constructed to commands and hebegan to look, to the untrained eye, as a relatively normal child byabout week 10.

Example 3 Male Child, 5V_Years Old

Male child, 5½ years of age with autism symptoms dating back to age ofaround 15 months—but diagnosed significantly later. The patientpresented initially with gastrointestinal symptoms in association withclassical autism—for treatment of the bowel symptoms. Although stooltest did not indicate any specific pathogen the bowel symptoms resembledthose of a chronic infection or adult Irritable Bowel Syndrome (IBS),i.e. intermittent diarrhea, constipation, cramping, colicky pain,inability to sleep at night, occasional explosive diarrhea andincontinence. The patient was treated with orthostatic lavage usingsodium pico-sulfate followed by water to produce voluminous diarrhea andto flush out the enteric contents. He was then given 125 mg Vancomycinthree times daily orally followed by oral re-colonization with bacteriaat a concentration of 10⁹ through to 10¹⁰, suspended in yoghurt—ofstrains which included bacteroides, Escherichia coli, and non-pathogenicClostridia—including Clostridium innocuum, bifermentans and ramosum. Theresponse was quite noticeable, in the reversal of the abnormal stoolfunction towards normality. The patient was also able to sleep throughthe night without any explosive diarrhea and produced formed stoolswithin five days of commencing the bacterial therapy. While thebacteriotherapy was continued the bowel symptoms were well controlled.Within 3-4 weeks of missing out the treatment for a week or two some ofthe symptoms would begin to recur. This suggested that the abnormalbacterial flora was suppressed rather than being cured with thistreatment in this patient. The unexpected finding however, was anoticeable and marked reversal of symptoms of autism. Whereas previouslyrepetitive movements were present with lack of eye contact, eye contactreturned fairly rapidly together with cessation of repetitive movementand progressive increase of word power from around 20 words to around600 words by the sixth month of treatment. The therapy continues now formore than 12 months with sustained reversal of autism and IBS symptoms.

Example 4 Male Child, 7 Years Old

A seven year old male patient was referred for treatment initially ofbowel problems. He had developed autism between age 1 and 2 yearscharacterized by lack of eye contact, repetitive movements, poorlydeveloped cognitive abilities, vocabulary of fewer than 20 words Themarked bowel symptoms were characterized by either constipation or largevoluminous motions, sometimes diarrhea and explosive stools. Stoolexamination was negative.

The patient was given a pre-treatment of Vancomycin 125 mg twice dailyand at one week he was given an orthostatic lavage consisting ofpicosulfate preparation which flushed out his bowel. He was then giventwice daily oral bacteriotherapy consisting of cultures containingliving probiotics. These included several bacteroides species,Escherichia coli and non-pathogenic Clostridia such as Clostridiumbutyricum, Clostridium bifermentans and Clostridium innocuum. Within twoweeks the bowel symptoms reversed to normal defecation with soft, formedstool—once or twice per day. Constipation disappeared, eye contactreturned over the next six weeks and vocabulary and word use quitedramatically improved, to everyone's surprise. When followed for eightmonths over 600 words could be counted in the vocabulary with sentencesof up to eight words being constructed where previously this was notpossible. Some abstract thinking was noted by teachers at the specialautism school. Parents in particular noted reduced aggression, greaterco-operation, and general increasing ability to develop a more normalrelationship with the child. Repetitive action also disappeared.

Example 5 Male Child, 6 Years Old

A male patient aged 6 was referred to the clinic for treatment ofchronic diarrhea and at times incontinence. The child had been autisticsince the age of one year and three months. The diagnosis however wasdelayed. He had slow cognitive development and very limited vocabulary.There was virtually absent eye contact and at times violent andexplosive behavior. The greatest problem with management was that ofcontrol of defecation as the child developed a fascination with thestools which would then be spread over furniture and walls. This broughtsevere pressure upon the family with respect to difficulty withmanagement. Stool test was collected and again was negative for anypathogen. The patient was given Vancomycin 250 mg twice daily for 10days after which a polyethylene glycol orthostatic lavage achieved alarge volume flush of the bowel. He was then given twice daily oralbacteriotherapy in a neutral yogurt as a carrier. Within one week thebowel function returned to virtual normality. However, the behavioralchanges were just as rapid in reversing again characterized by fairlyrapid reduction in aggressiveness and uncontrollable behavior, sleepingthrough the night, increased eye contact, and progressively increasedword power. The behavior of spreading stools also disappeared, more as abehavioral change than learnt phenomenon. The patient was continued onmedications for over a year and progressively improved in allparameters—at times fluctuating in severity.

What is claimed is:
 1. A pharmaceutical composition useful for thetreatment and/or prophylaxis of chronic disorders associated with thepresence in the gastrointestinal tract of a mammalian host of abnormalor an abnormal distribution of microflora, which composition comprises:(a) a viable non-pathogenic or an attenuated pathogenic Clostridia; and,(b) at least one additional bacterial species.
 2. The pharmaceuticalcomposition of claim 1, wherein: (a) the Clostridia is selected from thegroup consisting of Clostridium absonum, Clostridium argentinense,Clostridium baratii, Clostridium bifermentans, Clostridium botulinum,Clostridium butyricum, Clostridium cadaveris, Clostridium carnis,Clostridium celatum, Clostridium chauvoei, Clostridium clostridioforme,Clostridium cochlearium, Clostridium difficile, Clostridium fallax,Clostridium felsineum, Clostridium ghonii, Clostridium glycolicum,Clostridium haemolyticum, Clostridium hastiforme, Clostridiumhistolyticum, Clostridium indolis, Clostridium innocuum, Clostridiumirregulare, Clostridium limosum, Clostridium malenominatum, Clostridiumnovyi, Clostridium oroticum, Clostridium paraputrificum, Clostridiumperfringens, Clostridium piliforme, Clostridium putrefaciens,Clostridium putrificum, Clostridium ramosum, Clostridium sardiniense,Clostridium sartagoforme, Clostridium scindens, Clostridium septicum,Clostridium sordellii, Clostridium sphenoides, Clostridium spiroforme,Clostridium sporogenes, Clostridium subterminale, Clostridium symbiosum,Clostridium tertium, Clostridium tetani, Clostridium welchii, andClostridium villosum; (b) the at least one additional bacterial speciescomprises at least one strain of a viable non-pathogenic or anattenuated pathogenic Bacteroides; (c) the pharmaceutical composition of(b), wherein said Bacteroides is selected from the group consisting ofBacteroides caccae, Bacteroides capillosus, Bacteroides coagulans,Bacteroides distasonis, Bacteroides eggerthii, Bacteroides forsythus,Bacteroides fragilis, Bacteroides fragilis-ryhmä, Bacteroides gracilis,Bacteroides levii, Bacteroides macacae, Bacteroides merdae, Bacteroidesovatus, Bacteroides pneumosintes, Bacteroides putredinis, Bacteroidespyogenes, Bacteroides splanchnicus, Bacteroides stercoris, Bacteroidestectum, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroidesureolyticus, and Bacteroides vulgatus; (d) the at least one additionalbacterial species comprises one or more viable non-pathogenic orattenuated pathogenic bacteria comprising an anaerobic cocci; (e) the atleast one additional bacterial species comprises one or more viablenon-pathogenic or attenuated pathogenic bacteria selected from the groupconsisting of a Bacteroides, a Eubacteria, a Fusobacteria, aPropionibacteria, a Lactobacilli, an anaerobic cocci, a Ruminococcus, anEscherichia coli, a Gemmiger, a Desulfomonas, and a Peptostreptococcusspecies; (f) the pharmaceutical composition of (e), wherein the one ormore additional viable non-pathogenic or attenuated pathogenic bacteriacomprise a Bacteroides fragilis ss. Vulgatus, Eubacterium aerofaciens,Bacteroides fragilis ss. Thetaiotaomicron, Peptostreptococcus productusII, Bacteroides fragilis ss. Distasonis, Fusobacterium prausnitzii,Coprococcus eutactus, Eubacterium aerofaciens III, Peptostreptococcusproductus I, Ruminococcus bronii, Bifidobacterium adolescentis, Gemmigerformicilis, Bifidobacterium longum, Eubacterium siraeum, Ruminococcustorques, Eubacterium rectale III-H, Eubacterium rectale IV, Eubacteriumeligens, Bacteroides eggerthii, Clostridium leptum, Bacteroides fragilisss. A, Eubacterium biforme, Bifidobacterium infantis, Eubacteriumrectale III-F, Coprococcus comes, Bacteroides capillosus, Ruminococcusalbus, Eubacterium formicigenerans, Eubacterium hallii, Eubacteriumventriosum I, Fusobacterium russii, Ruminococcus obeum, Eubacteriumrectale II, Clostridium ramosum I, Lactobacillus leichmannii,Ruminococcus cailidus, Butyrivibrio crossotus, Acidaminococcusfermentans, Eubacterium ventriosum, Bacteroides fragilis ss. fragilis,Bacteroides AR, Coprococcus catus, Eubacterium hadrum, Eubacteriumcylindroides, Eubacterium ruminantium, Eubacterium CH-1, Staphylococcusepidermidis, Peptostreptococcus BL, Eubacterium limosum, Bacteroidespraeacutus, Bacteroides L, Fusobacterium mortiferum I, Fusobacteriumnaviforme, Clostridium innocuum, Clostridium ramosum, Propionibacteriumacnes, Ruminococcus flavefaciens, Ruminococcus AT, Peptococcus AU-1,Eubacterium AG, -AK, -AL, -AL-1, -AN; Bacteroides fragilis ss. ovatus,-ss. d, -ss. f; Bacteroides L-1, L-5; Fusobacterium nucleatum,Fusobacterium mortiferum, Escherichia coli, Streptococcus morbiliorum,Peptococcus magnus, Peptococcus G, -AU-2; Streptococcus intermedius,Ruminococcus lactaris, Ruminococcus CO Gemmiger X, Coprococcus BH, -CC;Eubacterium tenue, Eubacterium ramulus, Eubacterium AE, -AG-H, -AG-M,-AJ, -BN-1; Bacteroides clostridiiformis ss. clostridliformis,Bacteroides coagulans, Bacteroides orails, Bacteroides ruminicola ss.brevis, -ss. ruminicola, Bacteroides splanchnicus, Desuifomonas pigra,Bacteroides L-4, -N-i; Fusobacterium H, Lactobacillus G, orSuccinivibrio A; (g) the pharmaceutical composition further comprises afungi; (h) the pharmaceutical composition of (g), wherein the fungicomprises a Monilia (or Monilinia); (i) the pharmaceutical compositionfurther comprises at least one strain of a viable non-pathogenic or anattenuated pathogenic a Bifidobacterium; (j) the pharmaceuticalcomposition of (i), wherein the pharmaceutical composition comprises aClostridium innocuum, a Clostridium bifermentans, a Clostridiumbutyricum, a Bacteroides fragilis, a Bacteroides thetaiotaomicron, aBacteroides uniformis, one or more strains of an Escherichia coli, andone or more strains of a Lactobacillus; or (k) the pharmaceuticalcomposition of any one of (a) to (j), wherein the pharmaceuticalcomposition comprises a Clostridium bifermentans, a Clostridiuminnocuum, and a Clostridium butyricum in combination one or more strainsof an Escherichia coli, one or more strains of a Bacteroides and aPeptostreptococcus productus.
 3. The pharmaceutical composition of claim1, further comprising: (a) one or more additional agents; or (b) one ormore additional agents selected from the group consisting of an acidsuppressant, an antacid, an H2 antagonist, and a proton pump inhibitor.4. The pharmaceutical composition of claim 1, wherein the viablenon-pathogenic or the attenuated pathogenic Clostridia, or the at leastone additional bacterial species, are in the form of spores.
 5. Thepharmaceutical composition of claim 1, wherein: (a) the pharmaceuticalcomposition is lyophilized, pulverized and powdered or a liquid culture;(b) the pharmaceutical composition is in the form of or formulated as anenteric coated capsule, an enteric coated microcapsule, or a powdersuitable for reconstitution; (c) the pharmaceutical composition isformulated as or presented in the form of an enema; or (d) thepharmaceutical composition is formulated as or presented in the form ofa food, a food additive or food supplement; or (e) the pharmaceuticalcomposition of (d), wherein the food, food additive or food supplementcomprises or is formulated as a yogurt, a dairy-based product, asoy-based product, or a derivative thereof.
 6. A food, a food additiveor a food supplement comprising a pharmaceutical composition of claim 1.7. A method for the treatment and/or prophylaxis of a chronic disorderassociated with the presence in a gastrointestinal tract of a mammalianhost of an abnormal microflora or an abnormal distribution ofmicroflora, which method comprises: (a) providing a pharmaceuticalcomposition comprising a viable non-pathogenic or an attenuatedpathogenic Clostridia; and (b) administering to the mammalian host aneffective amount of the pharmaceutical composition of (a) for a periodof time sufficient to displace the abnormal microflora or abnormaldistribution of microflora.
 8. The method of claim 7, wherein: (a) theClostridia is selected from the group consisting of a Clostridiumabsonum, Clostridium argentinense, Clostridium baratii, Clostridiumbifermentans, Clostridium botulinum, Clostridium butyricum, Clostridiumcadaveris, Clostridium carnis, Clostridium celatum, Clostridiumchauvoei, Clostridium clostridioforme, Clostridium cochlearium,Clostridium difficile, Clostridium fallax, Clostridium felsineum,Clostridium ghonii, Clostridium glycolicum, Clostridium haemolyticum,Clostridium hastiforme, Clostridium histolyticum, Clostridium indolis,Clostridium innocuum, Clostridium irregulare, Clostridium limosum,Clostridium malenominatum, Clostridium novyi, Clostridium oroticum,Clostridium paraputrificum, Clostridium perfringens, Clostridiumpiliforme, Clostridium putrefaciens, Clostridium putrificum, Clostridiumramosum, Clostridium sardiniense, Clostridium sartagoforme, Clostridiumscindens, Clostridium septicum, Clostridium sordellii, Clostridiumsphenoides, Clostridium spiroforme, Clostridium sporogenes, Clostridiumsubterminale, Clostridium symbiosum, Clostridium tertium, Clostridiumtetani, Clostridium welchii, and a Clostridium villosum; (b) the methodfurther comprises administering at least one strain of a viablenon-pathogenic or an attenuated pathogenic Bacteroides; (c) the methodof (b), wherein the Bacteroides is selected from the group consisting ofa Bacteroides caccae, Bacteroides capillosus, Bacteroides coagulans,Bacteroides distasonis, Bacteroides eggerthii, Bacteroides forsythus,Bacteroides fragilis, Bacteroides fragilis-ryhmä, Bacteroides gracilis,Bacteroides levii, Bacteroides macacae, Bacteroides merdae, Bacteroidesovatus, Bacteroides pneumosintes, Bacteroides putredinis, Bacteroidespyogenes, Bacteroides splanchnicus, Bacteroides stercoris, Bacteroidestectum, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroidesureolyticus, and a Bacteroides vulgatus; (d) the method furthercomprises administering one or more additional anaerobic cocci; (e) themethod further comprises administering one or more additional viablenon-pathogenic or attenuated pathogenic microorganisms; (f) the methodof (e), wherein the one or more additional viable non-pathogenic orattenuated pathogenic microorganisms are selected from the groupconsisting of a Bacteroides, an Eubacteria, a Fusobacteria, aPropionibacteria, a Lactobacilli, a Ruminococcus, a Escherichia coli, aGemmiger, a Desuifomonas, and a Peptostreptococcus species; (g) themethod of (e), wherein the one or more additional viable non-pathogenicor attenuated pathogenic microorganisms are selected from the groupconsisting of a Bacteroides fragilis ss. Vulgatus, Eubacteriumaerofaciens, Bacteroides fragilis ss. Thetaiotaomicron,Peptostreptococcus productus II, Bacteroides fragilis ss. Distasonis,Fusobacterium prausnitzii, Coprococcus eutactus, Eubacterium aerofaciensIII, Peptostreptococcus productus I, Ruminococcus bronii,Bifidobacterium adolescentis, Gemmiger formicilis, Bifidobacteriumlongum, Eubacterium siraeum, Ruminococcus torques, Eubacterium rectaleIII-H, Eubacterium rectale IV, Eubacterium eligens, Bacteroideseggerthii, Clostridium leptum, Bacteroides fragilis ss. A, Eubacteriumbiforme, Bifidobacterium infantis, Eubacterium rectale III-F,Coprococcus comes, Bacteroides capillosus, Ruminococcus albus,Eubacterium formicigenerans, Eubacterium hallii, Eubacterium ventriosumI, Fusobacterium russii, Ruminococcus obeum, Eubacterium rectale II,Clostridium ramosum I, Lactobacillus leichmannii, Ruminococcus cailidus,Butyrivibrio crossotus, Acidaminococcus fermentans, Eubacteriumventriosum, Bacteroides fragilis ss. fragilis, Bacteroides AR,Coprococcus catus, Eubacterium hadrum, Eubacterium cylindroides,Eubacterium ruminantium, Eubacterium CH-1, Staphylococcus epidermidis,Peptostreptococcus BL, Eubacterium limosum, Bacteroides praeacutus,Bacteroides L, Fusobacterium mortiferum I, Fusobacterium naviforme,Clostridium innocuum, Clostridium ramosum, Propionibacterium acnes,Ruminococcus flavefaciens, Ruminococcus AT, Peptococcus AU-1,Eubacterium AG, -AK, -AL, -AL-1, -AN; Bacteroides fragilis ss. ovatus,-ss. d, -ss. f; Bacteroides L-1, L-5; Fusobacterium nucleatum,Fusobacterium mortiferum, Escherichia coli, Streptococcus morbiliorum,Peptococcus magnus, Peptococcus G, -AU-2; Streptococcus intermedius,Ruminococcus lactaris, Ruminococcus CO Gemmiger X, Coprococcus BH, -CC;Eubacterium tenue, Eubacterium ramulus, Eubacterium AE, -AG-H, -AG-M,-AJ, -BN-1; Bacteroides clostridiiformis ss. clostridliformis,Bacteroides coagulans, Bacteroides orails, Bacteroides ruminicola ss.brevis, -ss. ruminicola, Bacteroides splanchnicus, Desuifomonas pigra,Bacteroides L-4, -N-i; Fusobacterium H, Lactobacillus G, and aSuccinivibrio A; (h) the method further comprises administering a fungi;(i) the method of (h), wherein the fungi comprises a Monilia; (j) themethod further comprises administering at least one strain of viablenon-pathogenic or attenuated pathogenic Bifidobacterium; (k) wherein thepharmaceutical composition comprises a Clostridium innocuum, aClostridium bifermentans, a Clostridium butyricum, a Bacteroidesfragilis, a Bacteroides thetaiotaomicron, a Bacteroides uniformis, oneor more strains of an Escherichia coli, and one or more strains of aLactobacillus; (l) wherein the pharmaceutical composition comprises aClostridium bifermentans, a Clostridium innocuum, and a Clostridiumbutyricum in combination with one or more strains of an Escherichiacoli, one or more strains of a Bacteroides and a Peptostreptococcusproductus; (m) the method further comprises administering one or moreadditional agents; or (n) the method further comprises administering oneor more additional agents selected from the group consisting of an acidsuppressant, an antacid, an H2 antagonist, and a proton pump inhibitor.9. The method of claim 8, wherein the viable non-pathogenic or theattenuated pathogenic Clostridia, or the one or more additional viablenon-pathogenic or attenuated pathogenic microorganisms, are in the formof spores.
 10. The method of claim 7, wherein (a) the pharmaceuticalcomposition is lyophilized, pulverized and powdered or a liquid culture;(b) the pharmaceutical composition is formulated as or is administeredin a form selected from the group consisting of an enteric coatedcapsule, an enteric coated microcapsule, a reconstituted powder, anenema, a food, a food supplement, or a drink; or (c) the method of (b),wherein the food comprises a yogurt, a dairy-based product, a soy-basedproduct, or a derivative thereof.
 11. The method of claim 7, wherein themammalian host is a human.
 12. The method of claim 7, wherein: (a) themethod further comprises administration of an effective amount of atleast one antibiotic prior to administering the pharmaceuticalcomposition; (b) the method of (a), wherein the antibiotic comprises ananti-Clostridial antibiotic; or (c) the method of (b), wherein theanti-Clostridial antibiotic is selected from the group consisting of avancomycin, a rifampicin and a nitroimidazole.
 13. The method of claim7, wherein: (a) the method further comprises a nasogastric and/or anasoduodenal washout prior to administering the pharmaceuticalcomposition; or (b) administration is by one or more routes selectedfrom the group consisting of ingestion, parenteral infusion, enema,per-colonoscope, intubation of the small bowel and orally.
 14. Themethod of claim 7, wherein the chronic disorder is a gastrointestinaldisorder.
 15. The method of claim 7, wherein the chronic disorder is arheumatic disorder, an immune mediated disorder, or an auto-immunedisorder.
 16. The method of claim 7, wherein the chronic disorder is aneurological disorder or a regressive disorder.
 17. The method of claim7, wherein the chronic disorder is, a liver disorder, a psychiatricdisorder or a dermatological condition.
 18. The method of claim 7,wherein said regressive disorder is autism.
 19. The method of claim 7,wherein said disorder is sudden infant death syndrome (SIDS) or anorexianervosa.
 20. The method of claim 7, comprising a treatment regimen ofabout 10¹⁰ Clostridia cells per dose administered about 3 to 6 times perday for a period sufficient to stabilize the gut flora.